g_covar(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_covar(1)
NAME
g_covar - calculates and diagonalizes the covariance matrix
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_covar -f traj.xtc -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.log -ascii covar.dat -xpm covar.xpm
-xpma covara.xpm -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -xvg enum -[no]fit -[no]ref -[no]mwa -last int -[no]pbc
DESCRIPTION
g_covar calculates and diagonalizes the (mass-weighted) covariance matrix. All structures are fitted to the structure in the structure
file. When this is not a run input file periodicity will not be taken into account. When the fit and analysis groups are identical and the
analysis is non mass-weighted, the fit will also be non mass-weighted.
The eigenvectors are written to a trajectory file ( -v). When the same atoms are used for the fit and the covariance analysis, the refer-
ence structure for the fit is written first with t=-1. The average (or reference when -ref is used) structure is written with t=0, the
eigenvectors are written as frames with the eigenvector number as timestamp.
The eigenvectors can be analyzed with g_anaeig.
Option -ascii writes the whole covariance matrix to an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ...
Option -xpm writes the whole covariance matrix to an .xpm file.
Option -xpma writes the atomic covariance matrix to an .xpm file, i.e. for each atom pair the sum of the xx, yy and zz covariances is
written.
Note that the diagonalization of a matrix requires memory and time that will increase at least as fast as than the square of the number of
atoms involved. It is easy to run out of memory, in which case this tool will probably exit with a 'Segmentation fault'. You should con-
sider carefully whether a reduced set of atoms will meet your needs for lower costs.
FILES
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt.
Index file
-o eigenval.xvg Output
xvgr/xmgr file
-v eigenvec.trr Output
Full precision trajectory: trr trj cpt
-av average.pdb Output
Structure file: gro g96 pdb etc.
-l covar.log Output
Log file
-ascii covar.dat Output, Opt.
Generic data file
-xpm covar.xpm Output, Opt.
X PixMap compatible matrix file
-xpma covara.xpm Output, Opt.
X PixMap compatible matrix file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version info and quit
-nice int 19
Set the nicelevel
-b time 0
First frame (ps) to read from trajectory
-e time 0
Last frame (ps) to read from trajectory
-dt time 0
Only use frame when t MOD dt = first time (ps)
-tu enum ps
Time unit: fs, ps, ns, us, ms or s
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-[no]fityes
Fit to a reference structure
-[no]refno
Use the deviation from the conformation in the structure file instead of from the average
-[no]mwano
Mass-weighted covariance analysis
-last int -1
Last eigenvector to write away (-1 is till the last)
-[no]pbcyes
Apply corrections for periodic boundary conditions
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_covar(1)